The long-term research objective of Project 1 is to correlate molecular changes in DNA and RNA with establishment, progression, and metastasis of colon cancer. We will use three technologies developed in our laboratory: Multiplexed Ligase Detection Reaction (LDR) assays, Universal DNA arrays, and EndoV/DNA ligase mutation scanning assay. These technologies will identify point mutations, deletions, LOH, gene copy number, methylation status, and gene expression level in dozens of oncogenes and tumor suppressor genes within individual colon tumors. By capturing these genetic and epigenetic changes in important genes, the molecular profiles will allow us to identify new patterns and mechanisms of cancer gene activation and repression. Further, we will identify the genetic changes most important for metastatic progression to specific secondary sites, and in concert with Projects 2 and 3 construct and validate a molecular prognostic scoring system based upon genes that independently influence prognosis. Our specific aims are: (i), (ii) To identify important interactions between both known and putative oncogenes and tumor suppressor genes from (a) defined signaling pathways, and (b) candidate genes identified in adenocarcinomas and precursors by cDNA expression array analysis and prioritized in Project 2 and 3. Tumor sample (360 total), including aberrant crypts, adenomas, adenocarcinomas, liver and lung metastasis will be analyzed. We will use molecular changes in key genes from the p53, cell cycle, apoptosis, Wnt signaling, RPTK signaling, and TGFbeta signaling pathways as the foundation for interpreting how such changes provide a cell survival advantage, and contribute to progressive autonomous growth and metastasis of colon cancers. (iii) To ascertain which mutations or alterations in gene expression correlate with colon cancer metastasis, in (a) receptor protein kinases (RPTKs), their known ligands, and (b) candidate genes identified in liver and lung metastases and prioritized in Projects 2 and 3. We will identify the autocrine and paracrine activation loops mediated by specific RPTKs and their ligands in primary and metastatic tumors. (iv) To employ biostatistical and bioinformatic approaches (Project 3) to determine which alteration(s) identified in Projects 1 and 2, and Core B correlate with recurrence and survival. Two separate cohorts of resected Stage 2/3 primary colon cancers (400 total) with good and poor outcomes will be analyzed to identify and validate genes that independently influence prognosis.